Evidence map›Paper›PMID 31788681›Full record

ArticleLab on a chip2020

smFISH in chips: a microfluidic-based pipeline to quantify in situ gene expression in whole organisms.

Jason Wan, Gongchen Sun, Jocelyn Dicent, Dhaval S Patel, Hang Lu

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Lab on a chip, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.8field-weighted citation impact, top 28% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 11 citations in OpenAlex.

  1. HarnessingSensors (Basel, Switzerland) · 2025
    Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 1 institution in 2 countries.

Jason WanWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. hang.lu@gatech.edu and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-4434-9357
Gongchen SunSchool of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-7973-0422
Jocelyn DicentSchool of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
Dhaval S PatelSchool of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-1110-0125
Hang LuWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. hang.lu@gatech.edu and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-6881-660X
Georgia Institute of Technology · US

Funding

Systems variation underlying the genetics of agingR01AG056436 · NIA · UNIVERSITY OF OREGON · PI LU, HANG, PHILLIPS, PATRICK C. · 2017 to 2021
$2.7M
Quantitative microscopy-based rapid phenotyping and screeningR01GM088333 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI LU, HANG · 2011 to 2018
$2.3M
Quantitative Understanding of Mechnosensory Circuit on ChipR01NS096581 · NINDS · GEORGIA INSTITUTE OF TECHNOLOGY · PI LU, HANG · 2016 to 2020
$1.7M
NIA NIH HHS R01 AG056436NIGMS NIH HHS R01 GM088333NINDS NIH HHS R01 NS096581
6 · The paper itself

Abstract

Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-sequencing and RT-PCR) to compare gene expression levels in hypo- or hyper-morphic mutant animals (e.g. gain-of-function or knockout). This approach is limited, especially in complex gene networks, as these genetic mutations may affect the expressions of related genes in unforseen ways. In contrast, we developed a microfluidic-based pipeline to discover gene relationships in a single genetic background. The microfluidic device provides efficient reagent exchange and the ability to track individual animals. By automating a robust microfluidic reagent exchange strategy, we adapted and validated single molecule fluorescent in situ hybridization (smFISH) on-chip and combined this technology with live-imaging of fluorescent transcriptional reporters. Together, this multi-level information enabled us to quantify a gene expression relationship with single-animal resolution. While this microfluidic-based pipeline is optimized for live-imaging and smFISH C. elegans studies, the strategy is highly-adaptable to other biological models as well as combining other live and end-point biological assays, such as behavior-based toxicology screening and immunohistochemistry.

Indexed as

In Situ Hybridization, FluorescenceLab-On-A-Chip DevicesAnimalsCaenorhabditis elegansCaenorhabditis elegans ProteinsGene ExpressionGTP-Binding Protein alpha Subunits, Gi-GoTissue Culture TechniquesTransforming Growth Factor betaCaenorhabditis elegans ProteinsDAF-7 protein, C elegansgpa-3 protein, C elegansGTP-Binding Protein alpha Subunits, Gi-GoTransforming Growth Factor beta

Identifiers

PMID31788681
PMCPMC8146400
OpenAlexW2990746979

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.